Create Chromosome Ideogram w/ out reference genome

Question

[jake.gendron]

Hey guys,

I'm relatively new to R so bear with me. I'm trying to map gene locations to a chromosome, essentially looking at one chromosome at a time. I have looked at all the useful tools including Gviz, quantsmooth, and even in IdeoViz. The problem is I'm using Oryza sativa as my reference genome, and all of these packages require a separate download usually from UCSC which lacks my reference genome. Is there a way around this problem? I know essentially the length of Chr. 11 and have my data formatted as such.

Gene_ID         Chr   Start   End     Annotation
Os11t0100600-01 11  14258   16117   Alpha/beta hydrolase family protein.
Os11t0103050-00 11  127297  129067  Hypothetical protein.

Is there an easy was to get around this issue? Should I just create a box plot given the range of Chr 11 and then write a for loop to map each of the regions to their given location? I'm just struggling to find the simplest way to do this, so any help would be greatly appreciated.

Thanks

[steve]

you can just make the plots yourself custom if you know all the coordinates and chrom sizes you want to use; some guidelines for doing a custom ideogram/karyotype are here: Creating chromosome karyotype plot with R and ggplot2

Answer 1

[genecats.ucsc]

Usually the chromosome ideograms at UCSC indicate results of Giemsa staining experiments, not gene locations.

If you want to get a whole chromosome view of your data you could create an assembly hub, and create a simple 3 column bigBed file out of your data file, and the just look at the whole chromosome view of your bigBed in dense mode.

Creating an assembly is described here (there is a simple cytoband creation section as well): http://genomewiki.ucsc.edu/index.php/Assembly_Hubs

If you don't have web-accessible space available you can make all the necessary files and upload them to CyVerse as explained here: http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Hosting

and then view your assembly hub that way.

Lastly, you may also want to look into our list of automatically generated NCBI assembly hubs and see if any of the Oryza Sativa assembly hub there will work for your purposes (you may need to rename your chromosomes to match whatever NCBI uses): http://genome-test.cse.ucsc.edu/gbdb/hubs/genbank/plant/plant.ncbi.html

Please note that these automatically generated hubs are a work in progress and liable to change.

If you have further questions about UCSC data or tools feel free to send your question to one of the below mailing lists:

• General questions: [e-mail]
• Questions involving private data: [e-mail]
• Questions involving mirror sites: [e-mail]

ChrisL from the UCSC Genome Browser

Answer 2

[bernatgel]

If you have the length of your chromosomes or even an approximation, you should be able to plot them with karyoploteR.

You'd need to build a custom genome (a GenomicRanges object with one range per chromosome) and you should be good to go. You can find more information on how to plot a custom genome with karyoploteR and on how to plot the gene positions in the karyoploteR tutorial.